Intro to FreeSurfer Jargon

surface

volume

vertex

surface-based

cortical, subcortical

parcellation/segmentation

registration, morph, deform, transforms (computing vs. resampling)

surface

vertex

What FreeSurfer Does…

FreeSurfer creates computerized models of the brain from MRI data.

Input:

T1-weighted (MPRAGE)

1mm3 resolution

(.dcm)

Output:

Segmented & parcellated conformed

volume

(.mgz)

“recon your data”

…short for reconstruction

…cortical surface reconstruction

…shows up in command recon-all

Volumes

orig.mgz T1.mgz brainmask.mgz wm.mgz filled.mgz

(Subcortical Mass)

Cortical vs. Subcortical GM

coronal

sagittal

subcortical gmcortical gm

Cortical vs. Subcortical GM

coronal

sagittal

subcortical gm

Parcellation vs. Segmentation

(subcortical) segmentation(cortical) parcellation

surface

volume

vertex

surface-based

cortical, subcortical

parcellation/segmentation

registration, morph, deform, transforms (computing vs. resampling)

Registration

to find a common coordinate system for the input data sets

Examples:

comparing different MRI images of the same individual (longitudinal scans, diffusion vs functional scans)

comparing MRI images of different individuals

target

Inter-subject, uni-modal example

flirt 6 DOF

subject

flirt 9 DOF flirt 12 DOF

Linear registration: 6, 9, 12 DOF

Flirt 6 DOFFlirt 9 DOFFlirt 12 DOFsubjecttarget

targetsubjectFlirt 6 DOFFlirt 9 DOFFlirt 12 DOF

targetsubjectFlirt 6 DOFFlirt 9 DOF

Flirt 12 DOF

Intra-subject, multi-modal example

before spatial alignment

after spatial alignment

Inter-subject non-linear example

target CVS reg

Some registration vocabulary

Input datasets: Fixed / template / target Moving / subject

Transformation models rigid affine nonlinear

Objective / similarity functions

Applying the results deform, morph, resample, transform

Interpolation types (tri)linear nearest neighbor

FreeSurfer Questions

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to all your questions in the Glossary, FAQ, or

FreeSurfer Mailing List Archives

Intro to FreeSurfer Jargon - NRU · Intro to FreeSurfer Jargon surface. Intro to FreeSurfer Jargon...

Documents

FreeSurfer: Troubleshooting surfer.nmr.mgh.harvard

Function-Structure Integration in FreeSurferftp.nmr.mgh.harvard.edu/pub/docs/old_slides/freesurfer.func.pdf · Function-Structure Integration. FreeSurfer Registration FreeSurfer Subject-Specific

Introducon to FreeSurfer - wikis.la.utexas.eduwikis.la.utexas.edu/imagelab/sites/wikis.la.utexas... · Introducon to FreeSurfer ... EM Register (linear volumetric registration) 7

Freesurfer-based brain image analysis

FREESURFER HANDS-ON WORKSHOP

Working with FreeSurfer ROIs surfer.nmr.mgh.harvard.edu

(The Jargon Lexicon, watson-net/jargon/lexicon.asp)

Surface-based Group Analysis in FreeSurfer

Introducon to FreeSurfer - wikis.la.utexas.eduwikis.la.utexas.edu/imagelab/sites/wikis.la.utexas... · Introducon to FreeSurfer hp://surfer.nmr.mgh.harvard.edu Jenni Pacheco jpacheco@mail.utexas.edu

FreeSurfer Why use FreeSurfer? What happens? How do I do ... · • FreeSurfer can read/write: NIFTI, Analyze, MINC Careful with NIFTI! (has 32k limit; surfaces could be more) •

Introduction to FreeSurfer

3D Visualization of FreeSurfer Data

Intro to FreeSurfer Jargon voxel surface volume vertex surface-based recon cortical, subcortical parcellation/segmentation registration, morph, deform,

Working with FreeSurfer ROIs

Correction for multiple comparisons in FreeSurfer

Freesurfer Cortical Quality Check

Package 'freesurfer

FreeSurfer: Troubleshooting

Unix Tutorial for FreeSurfer Users. Helpful To Know FreeSurfer Tutorial Wiki: